An intrinsically disordered protein (IDP) does not have a definite 3D structure, and because of its highly flexible nature it evolves dynamically in very large and diverse regions of the phase space. A standard molecular dynamics run can sample only a limited region of the latter; even though this kind of simulation may be effective in sampling local temporary secondary structures, it is not sufficient to highlight properties that require a larger sampling of the phase space to be detected, like transient tertiary structures. But if the structure of an IDP is dynamically evolved using metadynamics (an algorithm that keeps track of the regions of the phase space already sampled), the system can be forced to wander in a much larger region of the phase space. We have applied this procedure to the simulation of tau, one of the largest totally disordered proteins. Combining the results of the simulation with small-angle X-ray scattering yields a significant improvement in the sampling of the phase space in comparison with standard molecular dynamics, and provides evidence of extended hairpin- and paperclip-like transient tertiary structures of the molecule. The more persistent tertiary pattern is a hairpin folding encompassing part of the N-terminal, the proline-rich domain, the former repeat and a functionally relevant part of the second repeat.

Battisti, A., Ciasca, G., Tenenbaum, A., Transient tertiary structures in tau, an intrinsically disordered protein, <<MOLECULAR SIMULATION>>, 2013; (39/13): 1084-1092. [doi:DOI:10.1080/08927022.2013.794275] [http://hdl.handle.net/10807/51985]

Transient tertiary structures in tau, an intrinsically disordered protein

Ciasca, Gabriele;
2013

Abstract

An intrinsically disordered protein (IDP) does not have a definite 3D structure, and because of its highly flexible nature it evolves dynamically in very large and diverse regions of the phase space. A standard molecular dynamics run can sample only a limited region of the latter; even though this kind of simulation may be effective in sampling local temporary secondary structures, it is not sufficient to highlight properties that require a larger sampling of the phase space to be detected, like transient tertiary structures. But if the structure of an IDP is dynamically evolved using metadynamics (an algorithm that keeps track of the regions of the phase space already sampled), the system can be forced to wander in a much larger region of the phase space. We have applied this procedure to the simulation of tau, one of the largest totally disordered proteins. Combining the results of the simulation with small-angle X-ray scattering yields a significant improvement in the sampling of the phase space in comparison with standard molecular dynamics, and provides evidence of extended hairpin- and paperclip-like transient tertiary structures of the molecule. The more persistent tertiary pattern is a hairpin folding encompassing part of the N-terminal, the proline-rich domain, the former repeat and a functionally relevant part of the second repeat.
2013
Inglese
Battisti, A., Ciasca, G., Tenenbaum, A., Transient tertiary structures in tau, an intrinsically disordered protein, <<MOLECULAR SIMULATION>>, 2013; (39/13): 1084-1092. [doi:DOI:10.1080/08927022.2013.794275] [http://hdl.handle.net/10807/51985]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10807/51985
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